Spoiler alert: the answer is not surprising
JeffinBranson asked in a comment what the DYAR numbers would look like for Rams legend, Kurt Warner. It is very difficult to do this on the same basis, because we don't have any PFF offensive line rankings for the GSOT seasons. I still thought it might be interesting to try to compare Warner and Peyton to Goff, so I did the best I could.
To estimate an OL rank, I took the adjusted line yard and adjusted sack rate numbers from Football Outsiders and averaged them. For the 1999 season, I also made an executive decision to add 70 DYAR points to the totals to try to adjust for "statistical creep" compared to 2019. It isn't clear whether this step is necessary and it isn't a very large change anyway, but I wanted to create as fair a comparison as possible. I came up with the number by estimating the average of the top 10 QBs for each season and comparing it for the 2 seasons. It didn't look to me like any adjustment was warranted for the subsequent years.
The 1999 season
If you went off the normal passing stats, you might think that Warner comes out way ahead, because he had 41 passing TDs, while Peyton only had 26. This isn't the case, because the raw DYAR numbers for the 2 QBs are nearly identical. Warner had 1,586 yards, leading the NFL, while Peyton was a close second place at 1,581 yards.
Both teams had very good OLs, with the Rams ranking 2nd in ALY. The adjustments for each QB were exactly the same, so obviously the final numbers remain super close.
Warner's adjusted DYAR: 1,456
Peyton's adjusted DYAR: 1,451
The 2000 season
Kurt Warner had a great start to 2000, but in the middle of the season he broke a finger on his throwing hand. When he returned later in the season, he only had 3TDs and 8 INTs. There is no such thing as an injury adjustment to DYAR, so all I can do is put an asterisk by his number, which fell to about half of his 1999 score. Kurt had the 7th best raw DYAR in the NFL in 2000, still very good despite his injury. The Rams had the best ALY in the NFL at 5.09. To this day, this is one of the best ALYs posted in a season. Some of that was the greatness of Marshall Faulk, league MVP that season. On the other hand, there's no way Warner scores so well in DYAR without Faulk, so maybe to some extent it balances out.
Peyton led the league with a raw DYAR of 1,882. The FO metrics made the offensive line one of the top units in the NFL, causing a penalty against this great score.
Warner's adjusted DYAR: 723
Peyton's adjusted DYAR: 1,582
The 2001 season
Warner rebounds and wins his 2nd MVP award this year. This was probably the best GSOT team. Some people say Warner wasn't as good in 2001 as 1999. Perhaps the reason they say this is because he had less TDs and way more INTs compared to 1999. There is more to the story than just regular stats.
Warner's adjusted DYAR is actually better in 2001 compared to 1999. This is despite me giving his 1999 number a slight boost that I didn't apply to the 2001 total. Warner had the best raw DYAR in the NFL at 1,790. The Rams once again had the best ALY in the league at 4.77. In my opinion, the 2001 Rams deserve to be considered among the greatest teams in NFL history.
Things weren't nearly so rosy for Peyton Manning and the Colts. They slumped to 6-10. This was Peyton's 4th NFL season. Jim Mora had his famous "Playoffs?!" post game press conference meltdown that season. Much of the team's struggles were blamed on a terrible defense and injuries on offense, but it bears emphasizing that the key thing that set Mora off in that game was Peyton Manning throwing a number of bad interceptions. Mora essentially throws Peyton under the bus and blames him for the loss. Unable to carry the Colts, Peyton had nearly as many interceptions (23) as TDs (26) in 2001.
The supposed definition of a franchise QB is that he can carry a team. Does the 2001 season prove that Peyton Manning was really a "system QB" because once he didn't have as much help around him, he wasn't nearly as good? Star RB, Edgerrin James tore his ACL, missing much of the season. Jerome Pathon had a foot injury and also missed most of the season. Reggie Wayne had a high ankle sprain in training camp. He still had Marvin Harrison, one of the greatest WRs of all time and they still had an excellent offensive line, but Peyton couldn't produce enough to get the Colts into the playoffs.
Warner's adjusted DYAR: 1,590
Peyton's adjusted DYAR: 765
Elvis has left the building
This ends up being a nice comparison, because it includes years 2 through 4 of Peyton Manning's career, mirroring the same seasons in Goff's career the last 3 seasons.
Warner's 3 year average adjusted DYAR: 1,256
Peyton's 3 year average adjusted DYAR: 1,266
Goff's 3 year average adjusted DYAR: 897
The difference is even greater if we throw out the odd "bad" seasons for Warner and Peyton. Only looking at the two good seasons, Warner and Peyton each average over 1,500 adjusted DYAR, a huge separation from Goff.
Of course, we're talking about the 2 best QBs from that 1999 to 2001 period and two future HOF QBs.
I don't know who would be 3rd best. I picked Brett Favre, because he looked like he might be the top candidate, and ran some numbers. He came out well behind Goff, so I eliminated every OL penalty, just used his raw DYARs and still gave him that small "stat creep" boost for 1999. Even with the most favorable treatment I could think of, Favre still comes out to an average DYAR of 835, which is lower than Goff's total.
Favre had a tremendous amount of continuity in his supporting talent during this period, consistent with how the Packers ran their franchise. Players such as Antonio Freeman, Bill Schroeder, Donald Driver, Corey Bradford, Dorsey Levens, Ahman Green, William Henderson and Bubba Franks. They also had outstanding OL talent, including Clifton, Wahle, Tauscher, Flanagan and Rivera. At one point, Wahle and Rivera were probably the best guard duo in the NFL. In the 2001 season playoffs, Favre throws 6 INTs against the Rams and the Packers were crushed 45-17.
If you are a Goff detractor, the QB from that era that I'd offer as a potential player comp would be Elvis Grbac. He had very good DYAR seasons in 1999 and 2000 playing for the Chiefs. Then, he signs as a free agent with the defending Super Bowl champion Ravens. They think they are upgrading the QB position over Trent Dilfer. The Ravens were on Hard Knocks that season. Star RB, Jamal Lewis, injures his knee in training camp (an incident that was featured in Hard Knocks.) Grbac had 18 INTs and only 15 TD passes that season. The Ravens still advanced to the divisional round of the playoffs, but it was Grbac's only season with the Ravens and his final year in the NFL.
How do Warner and Peyton compare to the other current QBs? If we took their best 2 seasons from 1999 to 2001 and compared it to the 2018 and 2019 list from my first fanpost in this series, Warner (3,046) and Peyton (3,033) would rank 2nd and 3rd behind Mahomes (3,351).